R Observatory: Metrics for beastier version 2.5.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

beastier

2.5.2Package record

Call 'BEAST2'

4packages depend

6.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Richèl J.C. BilderbeekCRAN page ↗GitHub ↗Website ↗Issues ↗rOpenSci review: issue 209 ↗

'BEAST2' (https://www.beast2.org) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is a command-line tool. This package provides a way to call 'BEAST2' from an 'R' function call.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("beastier", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("ropensci/beastier")

Development version from ropensci/beastier. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-beastier

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-beastier

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-beastier

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 4 earlier changesHide 4 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-04-06
ERROR13 OK, 1 ERROR2026-04-04
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.5.2

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 102 (1 internal)includes a package overview page
Examples that run: 100%76 run in a plain check
Exported functions with examples: 76%
Documented parameters: 100%
Return-value docs: 97%
Help pages citing references: 0%

Vignettes (1)

beastier demo HTML

How these are measured

Downloads

6.6K

CRAN downloads in the past year

Rank #5,818 · ~18/day · ~553/mo

Releases R versions

Daily download trend is not available in this view yet.

55330 days

1.4K90 days

6.6K1 year

Compare downloads with other packages →

Also on132 r2u25 autocran45 c2d4u

How downloads are counted

Repository

ropensci/beastier ↗Organization: ropensci

11Stars

1Forks

7Open issues

0Open PRs

54Releases

1,215Commits

5Commit identities

rr-packagerstatsbayesianbeastbeast2phylogenetic-inferencephylogenetics

License file reads as GPL-3.0 · 1,215 commits · Last activity 2025-12-08 · 0% stars, 30d · Default branch at 2.5.3, ahead of CRAN 2.5.2 (checked 2026-10-22)

Responsiveness

How these are sampled

PRs merged (all time): 75%
Median days to close, 50 most recently updated closed issues: 14
Median days to close, 50 most recently updated closed PRs: 38

Stars over time

2024-11-09 · 102026-07-07 · 11

How these are measured

PracticesBeta

11 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/ropensci/beastier on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Governance and community (4)

Code of conductContributing guideIssue templatesPR template

Coverage (1)

Coverage reporting (Codecov)

Research and citation (2)

CITATION.cffcodemeta.json

Show all practicesHide 1 practice

Lint, format, editor (2)

Lint workflowRStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing beastier adds 46 packages (29 with compiled code, 43 MB of source tarballs). Heaviest: stringi 11 MB, igraph 4.8 MB, sp 4.3 MB.

Depends (0)

none

Imports (11)

ape beautier phangorn rappdirs readr rJava rlang sessioninfo stringr tibble xml2

LinkingTo (0)

none

Suggests (5)

knitr rmarkdown spelling testthat tracerer (>= 2.2.3)

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

4direct

0indirect

Depends 1 · Imports 3

Depends, Imports or LinkingTo, most downloaded first

babette mauricer nodeSub mcbette

How these are counted

Code & Tests

People & History

People (6)

Richèl J.C. Bilderbeek

Author, Maintainer since 2.0.14 (2019)

Jason Griffiths

Contributor · added in 2.5.2

Thijs Janzen

Contributor · added in 2.1.1

Olivier Roy

Contributor · added in 2.5.1

Joëlle Barido-Sottani

Reviewer

Joëlle reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209

David Winter

Reviewer

David reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209

Releases (18)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
2.5.2Latest
record
2024-10-06 · current release · diff ↗
2.5.1
record
2024-06-04 · diff ↗
R
R 4.4.0 released · 2024-04-24
unarchivedReturned to CRAN
2023-11-07
2.5
record
2023-11-07 · diff ↗
archivedRemoved from CRAN
2023-10-24
requires archived package 'assertive'
2.4.12
record
2023-10-08 · diff ↗
R
R 4.3.0 released · 2023-04-21
unarchivedReturned to CRAN
2022-08-11
2.4.11
record
2022-08-11 · diff ↗ ·
removed 2 exports
create_beautier_tempfolder, remove_beautier_folder
archivedRemoved from CRAN
2022-08-08
requires archived package 'beautier'
2.4.10
record
2022-06-15 · diff ↗
2.4.9
record
2022-06-03 · diff ↗ ·
added 4 exports
check_empty_beaustier_folders, remove_beastier_folder, remove_beaustier_folders, remove_beautier_folder
R
R 4.2.0 released · 2022-04-22

Show 18 earlier eventsHide 18 earlier events

2.4.8
record
2021-09-19 · diff ↗
2.4.7
record
2021-09-07 · diff ↗ ·
added 8 exports
create_beast2_input_file_folder, create_beast2_screenlog_folder, create_beast2_state_output_file_folder, create_beast2_tracelog_folder, create_beast2_treelog_folder, create_beastier_tempfolder, create_beautier_tempfolder, extract_screenlog_filename_from_beast2_input_file
unarchivedReturned to CRAN
2021-08-19
2.4.6
record
2021-08-19 · diff ↗ ·
added 4 exports
check_empty_beastier_folder, extract_tracelog_filename_from_beast2_input_file, extract_treelog_filename_from_beast2_input_file, get_beastier_folder
archivedRemoved from CRAN
2021-07-13
policy violation Misuse of file system, e.g. ~/.beast
2.4.2
record
2021-06-05 · diff ↗ ·
added 1 export
get_beastier_tempfilename
2.4
record
2021-05-23 · diff ↗ ·
removed 8 exports
beast2_internal_filenames_to_table, check_beast2_internal_filenames, check_beast2_internal_filenames_data_types, check_beast2_internal_filenames_filenames_differ, check_beast2_internal_filenames_names, create_beast2_internal_filenames, print_beast2_internal_filenames, update_beastier

added 14 exports
add_quotes_if_has_spaces, check_can_create_dir_for_state_output_file, check_can_create_screenlog_file, check_can_create_state_output_file, check_can_create_tracelog_file, check_can_create_treelog_file, check_input_filename_validity, continue_beast2, create_beast2_continue_cmd_from_options, create_beast2_run_cmd_from_options, create_random_alignment, create_random_fasta, create_random_phylogeny, is_win_bin_path
R
R 4.1.0 released · 2021-05-18
2.2.1
record
2020-10-30 · diff ↗
2.2
record
2020-10-16 · diff ↗ ·
added 1 export
create_mcbette_beast2_options
unarchivedReturned to CRAN
2020-08-07
2.1.3
record
2020-08-07 · diff ↗ ·
added 10 exports
beastier_report, check_beast2_internal_filenames_data_types, check_beast2_internal_filenames_filenames_differ, check_beast2_internal_filenames_names, check_beast2_options_data_types, check_beast2_options_do_not_overwrite_existing_files, check_beast2_options_filenames_differ, check_beast2_options_names, get_default_beast2_version, rename_beast2_options_filenames
archivedRemoved from CRAN
2020-07-31
required archived package 'assertive'
R
R 4.0.0 released · 2020-04-24
2.1.1
record
2019-12-02 · diff ↗ ·
removed 4 exports
create_default_log_filename, create_default_trees_filenames, files_exist, get_alignment_ids

added 33 exports
are_beast2_input_lines_deep, are_beast2_input_lines_fast, are_identical_alignments, beast2_internal_filenames_to_table, beast2_options_to_table, check_beast2_internal_filenames, check_can_create_file, create_beast2_internal_filenames, create_beast2_version_cmd, create_beast2_version_cmd_bin, create_beast2_version_cmd_jar, create_temp_input_filename, create_temp_state_filename, get_alignment_ids_from_xml_filename, get_beast2_example_filename, get_beast2_example_filenames, get_beast2_main_class_name, get_beast2_options_filenames, get_beast2_version, get_default_beast2_download_url, get_default_beast2_download_url_linux, get_default_beast2_download_url_win, get_duplicate_param_ids, get_java_version, has_unique_ids, is_alignment, is_jar_path, print_beast2_internal_filenames, print_beast2_options, remove_file_if_present and 3 more
2.0.15
record
2019-06-02 · diff ↗
2.0.14
record
2019-05-31
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-05-31
Total releases: 18 / 7 yrs
License: GPL-3 OSI
Download size: 430 KB

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' entry:

citation("beastier")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1111/2041-210x.13032.

The repository also keeps a CITATION.cff.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for beastier version 2.5.2 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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